Valérian Méline on Transcriptomic and genomic analysis reveal new insights into tomato bacterial wilt resistance
Abstract. Ralstonia solanacearum is a devastating soil borne pathogen that causes bacterial wilt disease (BWD) in over 200 different plant species, including agriculturally important crops like tomato, banana, ginger and potato. Genetic resistance is considered the most efficient way to control this pathogen, but the underlying mechanisms and genes involved in resistance are not well described. In crops, resistance to Ralstonia is quantitative, and controlled by multiple genes with small effects. Here, we took two approaches to discover genes underlying resistance to Ralstonia in tomato, meta-transcriptomic analysis and Quantitative Trait Loci (QTL) analysis. Meta-transcriptomic analysis is an innovative computational approach that combines results from multiple independent studies to identify genes that consistently affect a trait of interest. We hypothesized that analyzing multiple genome-wide transcriptomes from tomato plants infected by Ralstonia in different experimental conditions would identify a common signature of tomato immune responses during BWD. Our results reveal the importance of water transport and receptor like kinases in tomato responses to Ralstonia. QTL analysis identifies regions of the genome that contribute to a trait of interest. This approach relies on large amount of phenotypic data to describe the trait of interest. Wilting is the major symptom of BWD and is challenging to phenotype, which may limit QTL detection. We developed a simple imaging platform and computational wilting metrics to quantify wilting from digital images. Using this system and a recombinant inbred line population of tomato, we digitally phenotyped nearly 1000 plants inoculated with a US strain of Ralstonia. We identify novel QTL as well as those that have been identified to other strains of Ralstonia. Together, these approaches improve our understanding of the underlying mechanisms and responsible genes of tomato resistance to Ralstonia.
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